Examples with Knowledge2 edu.cmu.tetrad.data.Knowledge2 used on opensource projects

Example 1 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class TestCpc method testSearch3.

/**
 * This will fail if the orientation loop doesn't continue after the first orientation.
 */
@Test
public void testSearch3() {
    IKnowledge knowledge = new Knowledge2();
    knowledge.setForbidden("B", "D");
    knowledge.setForbidden("D", "B");
    knowledge.setForbidden("C", "B");
    checkWithKnowledge("A-->B,C-->B,B-->D", "A---B,B-->C,D", /*"A-->B,C-->B,A-->D,C-->D",*/
    knowledge);
}

Example 2 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class GlassoRunner method getMeekRules.

public ImpliedOrientation getMeekRules() {
    MeekRules rules = new MeekRules();
    rules.setAggressivelyPreventCycles(this.isAggressivelyPreventCycles());
    rules.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    return rules;
}

Example 3 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class KpcRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    int depth = getParams().getInt("depth", -1);
    // Cpci pcSearch = new Cpci(getIndependenceTest(), knowledge, getIndependenceTest().getSimulatedData());
    Kpc kpc = new Kpc((DataSet) getDataModel(), getParams().getDouble("alpha", 0.001));
    kpc.setKnowledge(knowledge);
    kpc.setAggressivelyPreventCycles(isAggressivelyPreventCycles());
    kpc.setDepth(depth);
    Graph graph = kpc.search();
    System.out.println(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}

Example 4 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class MmhcRunner method execute.

// ============================PUBLIC METHODS==========================//
/**
 * Executes the algorithm, producing (at least) a result workbench. Must be
 * implemented in the extending class.
 */
public void execute() {
    Mmhc search;
    int depth = getParams().getInt("depth", -1);
    search = new Mmhc(getIndependenceTest(), getIndependenceTest().getDataSets().get(0));
    search.setDepth(depth);
    search.setKnowledge((IKnowledge) getParams().get("knowledge", new Knowledge2()));
    Graph graph = search.search();
    setResultGraph(graph);
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
}

Example 5 with Knowledge2

use of edu.cmu.tetrad.data.Knowledge2 in project tetrad by cmu-phil.

the class FasRunner method execute.

// ===================PUBLIC METHODS OVERRIDING ABSTRACT================//
public void execute() {
    IKnowledge knowledge = (IKnowledge) getParams().get("knowledge", new Knowledge2());
    int depth = getParams().getInt("depth", -1);
    Graph graph = new EdgeListGraph(getIndependenceTest().getVariables());
    Fas fas = new Fas(graph, getIndependenceTest());
    fas.setKnowledge(knowledge);
    fas.setDepth(depth);
    graph = fas.search();
    System.out.println(graph);
    for (Node node : graph.getNodes()) {
        System.out.println(node + " " + graph.getAdjacentNodes(node).size());
    }
    if (getSourceGraph() != null) {
        GraphUtils.arrangeBySourceGraph(graph, getSourceGraph());
    } else if (knowledge.isDefaultToKnowledgeLayout()) {
        SearchGraphUtils.arrangeByKnowledgeTiers(graph, knowledge);
    } else {
        GraphUtils.circleLayout(graph, 200, 200, 150);
    }
    setResultGraph(graph);
}